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A genome‐wide association study reveals a quantitative trait locus for days open on chromosome 2 in Japanese Black cattle

Sasaki, Shinji, Ibi, Takayuki, Kojima, Takatoshi, Sugimoto, Yoshikazu
Animal genetics 2016 v.47 no.1 pp. 102-105
Wagyu, alleles, calving, cattle, conception, days open, genetic variance, genome-wide association study, haplotypes, linkage disequilibrium, parathyroid hormone, quantitative trait loci, reproductive performance, single nucleotide polymorphism, telomeres
Days open (DO), which is the interval from calving to conception, is an important trait related to reproductive performance in cattle. To identify quantitative trait loci for DO in Japanese Black cattle, we conducted a genome‐wide association study with 33 303 single nucleotide polymorphisms (SNPs) using 459 animals with extreme DO values selected from a larger group of 15 488 animals. We identified a SNP on bovine chromosome 2 (BTA2) that was associated with DO. After imputation using phased haplotype data inferred from 586 812 SNPs of 1041 Japanese Black cattle, six SNPs associated with DO were located in an 8.5‐kb region of high linkage disequilibrium on BTA2. These SNPs were located on the telomeric side at a distance of 177 kb from the parathyroid hormone 2 receptor (PTH2R) gene. The association was replicated in a sample of 1778 animals. In the replicated population, the frequency of the reduced‐DO allele (Q) was 0.63, and it accounted for 1.72% of the total genetic variance. The effect of a Q‐to‐q allele substitution on DO was a decrease of 3.74 days. The results suggest that the Q allele could serve as a marker in Japanese Black cattle to select animals with superior DO performance.